style: update ruff configs

.github/workflows/checks.yml

@@ -34,4 +34,4 @@ jobs:
         run: python3 -m pip install ".[dev]"
 
       - name: Check style
-        run: python3 -m ruff check . && ruff format --check .
+        run: python3 -m ruff check . && python3 -m ruff format --check .

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
   - id: trailing-whitespace
   - id: end-of-file-fixer
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.2.0
+  rev: v0.5.0
   hooks:
     - id: ruff-format
     - id: ruff

README.md

@@ -17,7 +17,7 @@ The variation-normalization repo depends on VRS models, and therefore each varia
 | variation-normalization branch | variation-normalizer version | gene-normalizer version | VRS version |
 | ---- | --- | ---- | --- |
 | [main](https://github.com/cancervariants/variation-normalization/tree/main) | 0.6.X | 0.1.X | [1.X.X](https://github.com/ga4gh/vrs) |
-| [staging](https://github.com/cancervariants/variation-normalization/tree/staging) | 0.8.X | 0.3.X | [2.0-alpha](https://github.com/ga4gh/vrs/tree/2.0-alpha) |
+| [staging](https://github.com/cancervariants/variation-normalization/tree/staging) | >=0.8.X | >=0.3.X | [2.0-alpha](https://github.com/ga4gh/vrs/tree/2.0-alpha) |
 
 ## About
 

codebuild/deploy_eb_env.py

@@ -1,4 +1,5 @@
 """Module to deploy to staging EB environment."""
+
 import time
 
 import boto3

codebuild/deploy_eb_env_dev.py

@@ -1,4 +1,5 @@
 """Module to deploy to staging EB environment."""
+
 import time
 
 import boto3

codebuild/terminate_eb_env.py

@@ -1,4 +1,5 @@
 """Module for terminating EB staging environment."""
+
 import json
 import time
 

codebuild/terminate_eb_env_dev.py

@@ -1,4 +1,5 @@
 """Module for terminating EB staging environment."""
+
 import json
 import time
 

pyproject.toml

@@ -20,6 +20,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 requires-python = ">=3.8"
 description = "VICC normalization routine for variations"
@@ -39,7 +40,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 test = ["pytest>=6.0", "pytest-cov", "pytest-asyncio"]
-dev = ["pre-commit", "ruff==0.2.0", "psycopg2-binary", "jupyter", "ipykernel"]
+dev = ["pre-commit", "ruff==0.5.0", "psycopg2-binary", "jupyter", "ipykernel"]
 
 [project.urls]
 Homepage = "https://github.com/cancervariants/variation-normalization"
@@ -49,7 +50,7 @@ Source = "https://github.com/cancervariants/variation-normalization"
 "Bug Tracker" = "https://github.com/cancervariants/variation-normalization/issues"
 
 [build-system]
-requires = ["setuptools>=61.0"]
+requires = ["setuptools>=64"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.dynamic]
@@ -72,52 +73,62 @@ branch = true
 [tool.ruff]
 src = ["src"]
 
-lint.select = [
-  "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
-  "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
-  "I",  # https://docs.astral.sh/ruff/rules/#isort-i
-  "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
-  "D",  # https://docs.astral.sh/ruff/rules/#pydocstyle-d
-  "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
-  "ANN",  # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
-  "ASYNC",  # https://docs.astral.sh/ruff/rules/#flake8-async-async
-  "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
-  "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
-  "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
-  "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
-  "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-  "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-  "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
-  "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
-  "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
-  "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
-  "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
-  "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
-  "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
-  "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
-  "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
-  "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
-  "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
-  "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+[tool.ruff.lint]
+select = [
+    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
+    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
+    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
+    "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+    "D",  # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+    "ANN",  # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+    "ASYNC",  # https://docs.astral.sh/ruff/rules/#flake8-async-async
+    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+    "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+    "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+    "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
+    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+    "INP",  # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
+    "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+    "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
+    "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
+    "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
+    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+    "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+    "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
+    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+    "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
+    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+    "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
+    "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
+    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
 ]
-
-lint.fixable = [
-  "I",
-  "F401",
-  "D",
-  "UP",
-  "ANN",
-  "B",
-  "C4",
-  "G",
-  "PIE",
-  "PT",
-  "RSE",
-  "SIM",
-  "RUF"
+fixable = [
+    "I",
+    "F401",
+    "D",
+    "UP",
+    "ANN",
+    "B",
+    "C4",
+    "LOG",
+    "G",
+    "PIE",
+    "PT",
+    "RSE",
+    "SIM",
+    "PERF",
+    "FURB",
+    "RUF"
 ]
-# ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
+# ANN101 - missing-type-self
+# ANN102 - missing-type-cls
 # D203 - one-blank-line-before-class
 # D205 - blank-line-after-summary
 # D206 - indent-with-spaces*
@@ -131,9 +142,10 @@ lint.fixable = [
 # E501 - line-too-long*
 # W191 - tab-indentation*
 # PGH003 - blanket-type-ignore
+# S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
-lint.ignore = [
-  "ANN101", "ANN003",
+ignore = [
+  "ANN003", "ANN101", "ANN102",
   "D203", "D205", "D206", "D213", "D300", "D400", "D415",
   "E111", "E114", "E117", "E501",
   "W191",
@@ -146,14 +158,36 @@ lint.ignore = [
 # ANN2 - missing-return-type
 # ANN201 - Missing type annotation
 # ANN102 - missing-type-cls
+# ARG001 - unused-function-argument
+# D100 - undocumented-public-module
+# D102 - undocumented-public-class
 # N805 - invalid-first-argument-name-for-method
 # S101 - assert
+# SLF001 - private-member-access
 # B011 - assert-false
-# RUF001 - ambiguous-unicode-character-string
-"tests/*" = ["ANN001", "ANN102", "ANN2", "S101", "B011"]
+# INP001 - implicit-namespace-package
+# T201 - print
+"tests/*" = [
+    "ANN001",
+    "ANN102",
+    "ANN2",
+    "ARG001",
+    "D100",
+    "D102",
+    "S101",
+    "SLF001",
+    "B011",
+    "INP001"
+]
 "src/variation/schemas/*" = ["ANN001", "ANN201", "N805", "S101"]
-"codebuild/*" = ["T201"]
+"codebuild/*" = ["T201", "INP001"]
 
 [tool.ruff.lint.flake8-bugbear]
 # Allow default arguments like, e.g., `data: List[str] = fastapi.Query(None)`.
 extend-immutable-calls = ["fastapi.Query"]
+
+[tool.ruff.lint.flake8-annotations]
+mypy-init-return = true
+
+[tool.ruff.format]
+docstring-code-format = true

src/variation/__init__.py

@@ -1,4 +1,5 @@
 """The Variation Normalization package."""
+
 import logging
 from os import environ
 

src/variation/classifiers/__init__.py

@@ -1,4 +1,5 @@
 """Classifier package level import."""
+
 from .amplification_classifier import AmplificationClassifier
 from .cdna_deletion_classifier import CdnaDeletionClassifier
 from .cdna_delins_classifier import CdnaDelInsClassifier

src/variation/classifiers/amplification_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Amplification Classifier"""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/cdna_deletion_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Cdna Deletion Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/cdna_delins_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Cdna DelIns Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/cdna_insertion_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Cdna insertion Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/cdna_reference_agree_classifier.py

@@ -1,4 +1,5 @@
 """A module for the cDNA Reference Agree Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/cdna_substitution_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Cdna Substitution Classifier."""
+
 from typing import List, Optional
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/classifier.py

@@ -1,4 +1,5 @@
 """Module for Classification methods."""
+
 from abc import ABC, abstractmethod
 from typing import List, Optional
 
@@ -39,6 +40,6 @@ def can_classify(self, tokens: List[Token]) -> bool:
 
         for candidate in self.exact_match_candidates():
             if token_types == candidate:
-                exact_matches.append(candidate)
+                exact_matches.append(candidate)  # noqa: PERF401
 
         return len(exact_matches) == 1

src/variation/classifiers/genomic_deletion_ambiguous.py

@@ -1,4 +1,5 @@
 """A module for the Genomic Deletion Ambiguous Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/genomic_deletion_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Genomic Deletion Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/genomic_delins_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Genomic DelIns Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/genomic_duplication_ambiguous.py

@@ -1,4 +1,5 @@
 """A module for the Genomic Duplication Ambiguous Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/genomic_duplication_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Genomic Duplication Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/genomic_insertion_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Genomic Insertion Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/genomic_reference_agree_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Genomic Reference Agree Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/genomic_substitution_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Genomic Substitution Classifier."""
+
 from typing import List, Optional
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/gnomad_vcf_classifier.py

@@ -1,4 +1,5 @@
 """A module for the gnomAD VCF Classifier"""
+
 from typing import List, Optional, Union
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/hgvs_classifier.py

@@ -1,4 +1,5 @@
 """A module for the HGVS Classifier."""
+
 from re import Match, Pattern
 from typing import Dict, List, Optional
 

src/variation/classifiers/protein_deletion_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Protein Deletion Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/protein_delins_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Protein DelIns Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/protein_insertion_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Protein Insertion Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/protein_reference_agree.py

@@ -1,4 +1,5 @@
 """A module for the Reference Agree Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/protein_stop_gain_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Protein Stop Gain Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classifiers/protein_substitution_classifier.py

@@ -1,4 +1,5 @@
 """A module for the Protein Substitution Classifier."""
+
 from typing import List
 
 from variation.classifiers.classifier import Classifier

src/variation/classify.py

@@ -1,4 +1,5 @@
 """Module for classification."""
+
 from typing import ClassVar, List, Optional
 
 from variation.classifiers import (